Saccharomyces cerevisiae DNA Polymerase δ: High fidelity for base substitutions but lower fidelity for single-and multi-base deletions

John M. Fortune, Youri I Pavlov, Carrie M. Welch, Erik Johansson, Peter M J Burgers, Thomas A. Kunkel

Research output: Contribution to journalArticle

88 Citations (Scopus)

Abstract

Eukaryotic DNA polymerase δ (Pol δ) plays an essential role in replicating large nuclear genomes, a process that must be accurate to maintain stability over many generations. Based on kinetic studies of insertion of individual dNTPs opposite a template guanine, Pol δ is believed to have high selectivity for inserting correct nucleotides. This high selectivity, in conjunction with an intrinsic 3′-exonuclease activity, implies that Pol δ should have high base substitution fidelity. Here we demonstrate that the wild type Saccharomyces cerevisiae three-subunit Pol δ does indeed have high base substitution fidelity for the 12 possible base-base mismatches, producing on average less than 1.3 stable misincorporations/100,000 nucleotides polymerized. Measurements with exonuclease-deficient Pol δ confirm the high nucleotide selectivity of the polymerase and further indicate that proofreading enhances the base substitution fidelity of the wild type enzyme by at least 60-fold. However, Pol δ inefficiently proofreads single nucleotide deletion mismatches in homopolymeric runs, such that the error rate is 30 single nucleotide deletions/ 100,000 nucleotides polymerized. Moreover, wild type Pol δ frequently deletes larger numbers of nucleotides between distantly spaced direct repeats of three or more base pairs. Although wild type Pol δ and Pol ε both have high base substitution fidelity, Pol δ is much less accurate than Pol ε for deletions involving repetitive sequences. Thus, strand slippage during replication by wild type Pol δ may be a primary source of insertion and deletion mutagenesis in eukaryotic genomes.

Original languageEnglish (US)
Pages (from-to)29980-29987
Number of pages8
JournalJournal of Biological Chemistry
Volume280
Issue number33
DOIs
StatePublished - Aug 19 2005

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DNA-Directed DNA Polymerase
Yeast
Saccharomyces cerevisiae
Substitution reactions
Nucleotides
spleen exonuclease
Nucleic Acid Repetitive Sequences
Genes
Genome
Exonucleases
Mutagenesis
Guanine
Base Pairing
Kinetics
Enzymes

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Saccharomyces cerevisiae DNA Polymerase δ : High fidelity for base substitutions but lower fidelity for single-and multi-base deletions. / Fortune, John M.; Pavlov, Youri I; Welch, Carrie M.; Johansson, Erik; Burgers, Peter M J; Kunkel, Thomas A.

In: Journal of Biological Chemistry, Vol. 280, No. 33, 19.08.2005, p. 29980-29987.

Research output: Contribution to journalArticle

Fortune, John M. ; Pavlov, Youri I ; Welch, Carrie M. ; Johansson, Erik ; Burgers, Peter M J ; Kunkel, Thomas A. / Saccharomyces cerevisiae DNA Polymerase δ : High fidelity for base substitutions but lower fidelity for single-and multi-base deletions. In: Journal of Biological Chemistry. 2005 ; Vol. 280, No. 33. pp. 29980-29987.
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